You're right that GEDCOM uploading does cause more problems than manually entering data. That's part of the reason we limit the size of GEDCOMs you can upload at one time, and also limit how far back in time your GEDCOM upload can go.
But, as it is, some people don't like these limitations. I don't think the reaction would be very positive if we did away with GEDCOM imports altogether. :)
I also manually entered my data, because my Ancestry tree was started back when I didn't know online trees weren't reliable sources, so I wanted to start things off right on WikiTree. I'm glad I did, because it also forced me to go over all my research and I discovered a lot of new facts along the way. So I agree that that's the best way to do it!